A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of
Doctor of Philosophy in Life Sciences of the Nelson Mandela African Institution of
Science and Technology
Nubian ibex (Capra nubiana) is a wild goat species inhabiting the Sahara and Arabia deserts. C.
nubiana thrives well in its habitat which is characterized by intense solar radiation, high
temperatures, little feed, and water supply. The genetic basis of C. nubiana adaptation to its
environment remains unknown. Adaptive signatures of evolution in C. nubiana genome were
investigated using comparative genomics approaches. Paired-end sequence reads of three C.
nubiana individuals and other publicly available genome data were used for comparative genomic
analysis. Positive selection signals were detected from sequence alignment by comparing the rates
of synonymous versus non-synonymous substitutions (dN/dS) in orthologous protein-coding
genes shared by C. nubiana and related species using CodeML program in PAML package. Copy
number variations were detected from the sequence data using read-depth method, with the
domestic goat genome data acting as the reference. Genes involved in the skin barrier and hair
follicle development, such as ATP binding cassette subfamily A member 12 and UV stimulated
scaffold protein A, were found to be positively selected, suggesting that C. nubiana has evolved
adaptive mechanisms to cope with solar radiation and temperature extremes in its environment.
Additionally, a DNA repair gene (UV stimulated scaffold protein A) was reported to be under
strong selection signals, further supporting the assertion that C. nubiana has acquired adaptive
mechanisms to deal with possible DNA damages induced by prolonged exposure to solar
radiation. Similarly, duplications of viral response genes such as UL16 binding protein 3, Cluster
of Differentiation 48, Natural Killer Group 2D ligand 1-like, Bactericidal/permeability-increasing
fold containing family A, member 1, and Natural Killer Group 2D ligand 4-like were reported
in C. nubiana, indicating that it has acquired adaptive strategies to cope with viral stressors in its
environment. Additionally, xenobiotic compounds metabolism genes involved in
biotransformation (Cytochrome P450 2D6, carboxylesterase 1 and cytochrome P450 family 2
subfamily B member 6), conjugation (UDP Glucuronosyltransferase-2B7 and Glutathione S transferase Mu 4), and transport (Multidrug resistance protein 4) of toxic compounds were found
to be expanded in C. nubiana, suggesting possible adaptative mechanisms to desert diets that are
affluent in toxic compounds. This work represents the first effort to understand the genomic of
adaptations in C. nubiana, a wild African goat. The C. nubiana genomic information generated in
this study is an important resource for researchers seeking to find genes of interest for breeding
purposes among small ruminants of economic importance.